Abstract: An improved method for rapid identification of microorganisms is disclosed, along with sequences of PCR primers optimized for this purpose. The primers are designed based on information analysis of sequences from a large number of organism to amplify certain segments of genomic DNA whose sequences are unique among different organisms. The PCR products are compared with a DNA sequence database to obtain the identity of the microorganisms. This approach provides an accurate and fast identification and taxonomic assignment of microbial species.

Abstract: Method of preparing a biological sample appropriate for use in a subsequent in vitro nucleic acid amplification reaction. The method involves a rapid, transient exposure to alkaline conditions which can be achieved by mixing an alkaline solution with a pH-buffered solution that includes a detergent and the biological sample to be tested for the presence of particular nucleic acid species using in vitro amplification. The invented method advantageously can improve detection of some target nucleic acids without substantially compromising detectability of others. The method is particularly useful for simultaneously preparing RNA and DNA templates that can be used in multiplex amplification reactions.

Abstract: The present invention provides an isolated oligonucleotide and a method using the isolated oligonucleotide to detect and/or identify at least two polynucleotides from a nucleic acid-protein complex. The oligonucleotide comprises at least one first tag and at least one second tag, wherein the first and second tags are obtained from a nucleic acid-protein complex.

Abstract: A method for detecting viable cells such as bacterial cells, within a sample, said method comprising (i) incubating said sample with a virus which is able to infect said cells under conditions which allow said virus to infect and replicate within any such cells which are viable; (ii) detecting any nucleic acid obtained by replication of the virus in said cell.

Abstract: A method for synthesizing cDNA possessing a consecutive sequence starting with a nucleotide adjacent to a cap structure of mRNA, which comprises (i) a process for annealing a double-stranded DNA primer and an RNA mixture containing mRNA possessing a cap structure, (ii) a process for preparing a conjugate of an mRNA/cDNA heteroduplex and a double-stranded DNA primer by synthesizing the first-strand cDNA primed with the double-stranded DNA primer using reverse transcriptase, and (iii) a process for circularizing the conjugate of the mRNA/cDNA heteroduplex and the double-stranded DNA primer by joining the 3? and 5? ends of the DNA strand containing cDNA using ligase. This method enables us to efficiently synthesize a full-length cDNA possessing a consecutive sequence starting with a transcription-start-site nucleotide from a small amount of RNA by small processes.

Abstract: This invention provides compositions and methods for HCV typing, e.g., genotyping and/or subtyping. The compositions and methods of the invention can be used to assign an HCV isolate to one of at least five HCV types (for example, selected from types 1, 2, 3, 4, 5 or 6), or to one of at least five subtypes (for example, subtypes 1a/b/c, 2a/c, 2b, 3a, 4a, 5a or 6a). These methods integrate the hybridization data from a plurality of HCV typing probes in a multidimensional analysis to make an HCV type assignment for an HCV in an experimental sample. The invention also provides related compositions, including, for example, the HCV typing probes and HCV typing diagnostic kits.

Abstract: An extraction and analysis device includes a microfluidic based collection system that extracts one or more different analytes from a fluid-based sample and an optical analysis system directly coupled to the collection system to perform optical analysis on the one or more collected analytes. The microfluidic based collection system includes microfluidic circuitry for directing a fluid based sample to a purification chip. Analytes collected within the purification chip can be either subsequently removed and analyzed or the analytes can be analyzed directly, while still within the purification chip, using the optical analysis system. The purification chip is preferably comprised of a plurality of pillars, the surface area of each pillar is coated with a specific capture chemistry. The specific capture chemistry is applied by derivitizing the pillars such that a ligand, such as a nucleic acid, an amptimer, or an antibody is attached to each pillar.

Abstract: The invention relates to a process for isolation of plasmid DNA from biomass by means of an aqueous 2-phase system having a polymer component and a salt component, characterized in that the resuspension of the biomass employed, the alkaline lysis of the biomass, the neutralization of the alkaline lysis batch and the separation of the plasmid DNA from the contaminants are carried out in a single reaction vessel (one-pot process) rendered possible in that the neutralization of the alkaline lysis batch is carried out in one and the same container by addition of potassium phosphate and one component of the aqueous 2-phase system is therefore already present. The second component of the aqueous 2-phase system is a PEG having a molecular weight of the mathematical average of about 600 g/mol to 1,000 g/mol.

Abstract: A process is provided to generate fluorescent molecules in the presence of target nucleic acids, but not in the absence of that target. Two probes, one bearing moiety A and the other bearing moiety B, bind to the target in a way that brings A and B together. A photon then converts A into A*, which can react with B to form a new species Z that is fluorescent. If A* does not encounter B, then A* reverts to form A. This allows the probe to have another opportunity to be activated should it be later bound near B. In one embodiment, a photoenolization creates A* as a diene; this reacts with a dienophile B in a Diels-Alder reaction. The linker Z may cause the linked probes to bind less tightly to the target, allowing the target to generate many fluorescent products, or be read through by a polymerase.

Abstract: The present invention relates to methods, compositions and kits for determining the prognosis of a clinical response in a human patient to a medicament which acts in the central nervous system and which is a substrate of the ABCB1 protein. Further, the invention relates to a combination of medicaments for the treatment of human patients having specific polymorphisms in the ABCB1 gene.

Abstract: Methods are described herein for detecting and identifying distinct species of nucleic acids, in a single container, for example, from a certain genus of infectious agents or otherwise causative agents comprising, for example, providing a forward PCR primer common to a homologous gene region between the distinct species, and providing a reverse PCR primer common to a homologous gene region between the distinct species, to thereby define a PCR target region amongst the species, and providing a first oligonucleotide probe specific to a nucleic acid sequence within the target region that is characteristic of a first species, providing a second oligonucleotide probe specific to a nucleic acid sequence within the target region that is characteristic of a second species, wherein the first and second oligonucleotide probes are each detectably labeled with distinctly different detectable labels, conducting a PCR reaction in the container by means of the primers to amplify the target region amongst the species, and de

Abstract: The present invention relates to a nucleic acid ligands capable of binding to one or more target molecules in a complex mixture.

Abstract: Provided herein is a method for the quantitative detection of HHV-6 subtypes A and/or B based on the use of a calibrator, suitable primers and probes, and a nucleic acid polymerase with 5?-3? nuclease activity.

Abstract: The invention is generally directed to a physiogenomic method for predicting diabetes and metabolic syndromes induced by psychotropic drugs. In one embodiment, the invention relates to the use of genetic variants of marker genes to predict the likelihood that an individual will experience undesirable metabolic side effects as a result of the use of a drug including, but not limited to, psychotropic drugs. The invention also relates to methods predicting the likelihood of diabetes and metabolic syndromes induced by the use of drugs with undesirable metabolic side effects.

Abstract: A protein detecting device, which comprises: (1) a detecting unit having a bonding section, which has properties for specifically bonding to a protein to be detected, a detecting section for detecting the bonding of the protein to be detected to the bonding section, the detecting section being made up of a polynucleotide double strand and a charge separating group, and an electrode section detecting the change in electrical conductivity of, or amount of transferred charge in, the polynucleotide double strand modified by the bond of the protein, (2) a standard electrode, (3) a reference electrode, (4) a container for housing the detecting unit, the standard electrode and the reference electrode, and containing a sample solutions comprising the protein to be detected, and (5) a measuring unit for measuring the protein based on a signal detected in the detecting unit.

Abstract: Disclosed are oligonucleotides useful in methods for determining whether a sample contains Cryptococcus neoformans, a causative agent for human cryptococcosis. These oligonucleotides, which have nucleotide sequences derived from a coding segment of the gene encoding the fungal specific transcription factor gene in Cryptococcus neoformans, are useful as forward and reverse primers for a polymerase chain reaction using nucleic acids from a biological sample as templates, and as probes for detecting any resultant amplicon. Detection of an amplicon indicates the sample contains Cryptococcus neoformans. Real-time PCR and detection using florescence resonance energy transfer is disclosed.

Abstract: The invention generally relates to methods for detecting a target nucleic acid and a target protein in a single assay.

Abstract: The present invention provides a method for obtaining thermostable enzymes. The present invention also provides variants of DNA polymerase I from Thermus aquaticus. The present invention further provides methods of identifying mutant DNA polymerases having enhanced catalytic activity. The present invention also provides polynucleotides, expression systems, and host cells encoding the mutant DNA polymerases. Still further, the present invention provides a method to carry out reverse transcriptase-polymerase chain reaction (RT-PCR) and kits to facilitate the same.

Abstract: This invention provides compositions and methods for HCV typing, e.g., genotyping and/or subtyping. The compositions and methods of the invention can be used to assign an HCV isolate to one of at least five HCV genotypes (for example, selected from genotypes 1, 2, 3, 4, 5 or 6), or assign an HCV isolate to one of at least six subtypes (for example, selected from subtypes 1a/b/c, 2a/c, 2b, 3a, 4a, 5a or 6a), where the methods of the invention use only a single typing probe to make the HCV type assignment.

Abstract: Five protein families cooperate to form the warhead structure that characterizes enediyne compounds, both chromoprotein enediynes and non-chromoprotein enediynes. The protein families include a polyketide synthase and thioesterase protein which form a polyketide synthase catalytic complex involved in warhead formation in enediynes. Genes encoding a member of each of the five protein families are found in all enediyne biosynthetic loci. The genes and proteins may be used in genetic engineering applications to design new enediyne compounds and in methods to identify new enediyne biosynthetic loci.